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Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

Kale S, Sode O, Weare J, Dinner AR - J Chem Theory Comput (2014)

Bottom Line: Chem.Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations.The approach also shows promise for free energy calculations when thermal noise can be controlled.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States.

ABSTRACT

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled.

No MeSH data available.


Related in: MedlinePlus

Reaction pathwaysfor malonaldehyde tautomerization after 100 R-or P-only (A) or 20 ML (B) iterations of refinement.
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fig3: Reaction pathwaysfor malonaldehyde tautomerization after 100 R-or P-only (A) or 20 ML (B) iterations of refinement.

Mentions: The enol of malonaldehydecan undergo intramolecular proton transfers (Figure 1). Estimates for the hopping barrier vary with the level oftheory, from 0.9 to 3.7 kcal/mol with DFT functionals37 to 3.9–4.4 kcal/mol with coupled cluster approaches.19,37,38 Hartree–Fock and earlySE methods overestimate this and similar conversion barriers, probablyas a result of underestimating electron correlation, and, consequently,also, the stabilization from conjugation in the transition state.39,40 We tested four protocols, an R-only one with the BLYP functional(black, Figure 3), and three ML runs with SEpreconditioners PM3 (red), PM6 (green), and SCC-DFTB (blue).


Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

Kale S, Sode O, Weare J, Dinner AR - J Chem Theory Comput (2014)

Reaction pathwaysfor malonaldehyde tautomerization after 100 R-or P-only (A) or 20 ML (B) iterations of refinement.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263463&req=5

fig3: Reaction pathwaysfor malonaldehyde tautomerization after 100 R-or P-only (A) or 20 ML (B) iterations of refinement.
Mentions: The enol of malonaldehydecan undergo intramolecular proton transfers (Figure 1). Estimates for the hopping barrier vary with the level oftheory, from 0.9 to 3.7 kcal/mol with DFT functionals37 to 3.9–4.4 kcal/mol with coupled cluster approaches.19,37,38 Hartree–Fock and earlySE methods overestimate this and similar conversion barriers, probablyas a result of underestimating electron correlation, and, consequently,also, the stabilization from conjugation in the transition state.39,40 We tested four protocols, an R-only one with the BLYP functional(black, Figure 3), and three ML runs with SEpreconditioners PM3 (red), PM6 (green), and SCC-DFTB (blue).

Bottom Line: Chem.Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations.The approach also shows promise for free energy calculations when thermal noise can be controlled.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States.

ABSTRACT

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled.

No MeSH data available.


Related in: MedlinePlus